Structure of a Tethered Cationic 3-Aminopropyl Chain Incorporated into an Oligodeoxynucleotide:  Evidence for 3‘-Orientation in the Major Groove Accompanied by DNA Bending

The structure of the dodecamer d(CGCGAATXCGCG)₂, in which X = Z3dU, 5-(3-aminopropyl)-2‘-deoxyuridine, was determined. At neutral pH, Z3dU introduced a positive charge into the major groove. NMR spectroscopy revealed that the Z3dU ω-aminopropyl moiety oriented in the 3‘-direction from the site of modification. Watson−Crick base pairing remained intact throughout the dodecamer. The presence of the charged amino group in the major groove resulted in a 0.24 ppm upfield shift of one ³¹P NMR resonance in the 3‘-direction at the phosphodiester linkage between nucleotides C⁹ and G¹⁰. Molecular dynamics calculations restrained by distances obtained from ¹H NOE data and torsion angles obtained from ¹H NMR ³J coupling data, and in which the ω-amino group was constrained to be proximate to G¹⁰O⁶, predicted from the ³¹P NMR data and molecular modeling (Dande, P.; Liang, G.; Chen, F.-X.; Roberts, C.; Nelson, M. G.; Hashimoto, H.; Switzer, C.; Gold, B. Biochemistry 1997, 36, 6024−6032), were consistent with experimental NOEs. These refined structures exhibited bending. The distance from the amino group to the 5‘-phosphate oxygen of Z3dU was >5 Å, which indicated that in this dodecamer the Z3dU amino group did not participate in a salt bridge to its 5‘-phosphate.